(March, 2007)
Once the data has been integrated by SAINT, there will be a series of data files in the (smartuser)(apexuser)/mydir subdirectory in which you are operating. These need to be further converted before you can use them with either TEXSAN or SHELXTL. In the process we will also apply corrections for crystal decay (which is very rare in the way that we usually take data) and for absorption (which is common, even on weakly absorbing crystals, due to the diffraction geometry which we use). We also want to get some information about our data set and crystal; space group, density, statistics, etc. There are two programs which we use for this purpose, XPREP and SADABS. For the purposes of this exercise the raw filenames are filename0.raw, filename1.raw, filename2.raw, filename3.raw, and filenamem.raw.
Normally we will run XPREP
to determine space group, density and absorption coefficient and to
test
the effects of absorption. It is then recommended that you use SADABS
on the data set to apply a different type of absorption correction and
also
to allow it to do the other things that it does to the data. SADABS is a release version of
the program, but much of what it does is mysterious. It is
significantly
better than XPREP in cases of high absorption or other
problems,
but not much different in well-behaved cases. If you have really
serious absorption you will need to do a face-indexed absorption correction.
XPREP is a prgram developed
by George Sheldrick. It is designed to perform space group
analyses, apply absorption corrections, and examine your data in a
number of useful ways (Laue patterns, reflection measurements at
differnt resolution shells and so-on). There is documentation of older
versions included in the SHELXTL suite of software. It reads either
raw data files from SAINT or hkl files from other programs such
as
SADABS. It also reads P4P files to get information about the crystal.
It writes a file with extension PRP (i.e. filenamem.prp), which is a
printable output file,
and optionally writes other hkl files. What follows here is an
abbreviated description. We start the program as follows.
For the purposes of these
examples, we will use "smartuse" to define the user/instrument on which
you collected data. It can be substituted with apexuser if you
collected data on the APEX instrument.
<...smartuse/mydir> % xprep filenamem <CR>
XPREP assumes either an hkl
or raw extension to the file name.
If you forget to give the
filename, and just type xprep,
XPREP will ask for a filename.
You have to specify the extension. Type: filenamem.raw. If you
have had to enter the filename separately you will then be prompted for
which type of data format the file is in select: "[4] SHELX HKLF 4 format or SAINT
._rf file".
The program will read the raw
data file, and also the file filenamem.p4p
to get information about the cell. In the interaction which follows,
there will always be a default value for a response which will be shown
by the program in square brackets, [xx]. To select the
default
response, just hit <CR>. However, you do not always want
the default response.
Be sure to read what the display says and react accordingly.
XPREP will show you
displays which are designed to allow you and it to choose the space
group. You should be aware that XPREP is very conservative about
choosing a space group, and that it misses even P21/c on a
regular basis. You may very well need to force it to take the correct
space group.
The following is a
step-by-step analysis of each window and what is going on within XPREP.
First you will see an
analysis of the data to determine the lattice type. Usually the
default (highlighted in brackets) is acceptable.
You will then be prompted for
a search for Higher Metric Symmetry [H],
followed by output for the reduced cell parameters. You will
often be given several options for what the Laue group is. Select
the most appropriate (again usually the default).
You will then begin a space
group analysis [S]. The
lattice type is re-determined and you will be shown a list of
systematic absences. Examine these and determine if XPREP has
obtained the correct space group. Often there will be several
choices. use your knowledge and best judgement to determine if
the correct space group has been selected. If not, select it
yourself. Be aware of any potential cell transformations.
You may need to lie to the program for purposes of absorption
correction.
XPREP will then perform a
low-level data analysis [D].
Accept the defaults but be sure to examine the analysis of the data at
various resolution shells, for completeness, R(int) and R(sym).
You have to go through this process or XPREP will return here until
this routine is performed.
You will return to the main
menu and be prompted to input the Cell Contents [C]. enter this routine and
fill in the molecular formula as best you are able. Note: XPREP
utilises some common naming conventions for various groups (Me =
methyl, Et = ethyl etc). You can also enter molecules separated
into moieties by enclosing them in parentheses. This allows input
of multiple of the same type of moiety (if present in your molecules)
by including the number of such groups AFTER the parentheses.
XPREP will calculate mu, the absorption coefficient. Note the
value down somewhere so that you can calculate mu*r or mu*t for the
absorptioin corrections.
WARNING: In order to do an absorption correction correctly, the cell must NOT be transformed before the correction is applied. Frequently the correct choice of space group will result in an un-announced transformation of the unit cell. Check the Matrix section of the output periodically to make sure that the cell has not been transformed without your consent. It may be necessary to lie to the program about your space group, at least initially, to get it to leave your cell alone. (Note that this lie does absolutely no damage to your data, since TeXsan will re-determine your space group and appropriate cell transformation when it processes the data.)
After you have entered the
cell contents, the next step is to check absorption using the [A]
option at the main menu. The official "type" of absorption correction
is Psi
Scan [P]. You
will then be prompted with:
Psi and raw data MUST be
indexed on original cell !
<Enter> to abort now, 'C' to continue:
Press C <CR> to
continue the absorption correction process.
You will then be prompted for
the wavelength at which the data were collected. The default is
correct for data colleted on our laboratory instruments.
The tolerance for direction cosines should be set to 0.05, the default of 0.01 is a bit too conservative and you should change the I/sigma cutoff to 10.0.
The usual empirical correction type is Ellipsoid [E], and you will have to input a value for mu*R, the absorption coefficient times the mean radius of your crystal. It is an observed fact for this kind of correction that the radius should be weighted towards the smaller half-dimensions of the crystal. You should also calculate the value of e-mu*t for your minimum crystal thickness. Compare this result to the value of Tmax which is given by the calculation. They should be about the same (i.e. 0.95 is about the same as 0.90). If they are, then the correction should be a reasonable one, and should be applied. Please do not select "print the reflections", as this makes the output file very long.
Once you have applied the
absorption correction, or decided that one is not appropriate, return
to
the main menu and write the hkl file [F].
You will then be prompted for an output filename, the default usually
suffices followed by a query about the file format. Make sure to
select the XS/SHELXS [S]
format. It is the default. Lastly you will need to write
(overwrite) the HKL file [Y].
Press <CR> to write the
HKL file.
To quit XPREP press Q <CR> at the main screen
(this is the default after you have follwoed this procedure).
Print the results of your analysis by typing
<...smartuse/mydir> %print filenamem.prp<CR>
SADABS requires the files filename0.raw, filename1.raw, filename2.raw, and filename3.raw.
In the following example,
everything except the bold words are printed by the program. (Bold-face
parenthetical remarks to clarify what is going on are not part of the
computer output.) The numbers are taken from an actual example, but
the filenames have been changed to protect the guilty. Your numbers
will
be different. For a more detailed discussion of the SADABS
program and how it applies corrections to data, view the SADABS manual.
<...smartuse/mydir> % sadabs<CR>
SADABS - Bruker area detector absorption (and other) corrections
-----------------------------------------------------------------
Maximum number of reflections
allowed (500000): <CR>
Enter listing filename [sad.abs]: filenames.out<CR>
(Note that the use of the substitution of "s" for "m" in the file names. This is conventional but not necessary. Just don't use the identical name to what you have been using before.)
Laue group numbers:
[1] -1................................................... [8] -3m (rhombohedral axes)
[2] 2/m (Y unique).............................. [9] -31m (Z unique)
[3] mmm ........................................... [10] -3m1 (Z unique)
[4] 4/m (Z unique)............................ [11] 6/m (Z unique)
[5] 4/mmm (Z unique)...................... [12] 6/mmm (Z unique)
[6] -3 (rhombohedral axes)............. [13] m3
[7] -3 (Z unique).............................. [14] m3m
Enter Laue group number [2]: nn<CR> --- (Pick the correct number and input it.)
Treat Friedel opposites as equivalent for parameter refinement (Y or N) ?
If you answer with Y, you may suppress the anomalous differences, but for N a higher redundancy is needed for a good correction. A chiral space group is assumed for the answer N [Y]: <CR>
(In fact, even if you have
a chiral space group with anomalous scatterers, it is a good idea to
use
the default here. The changes induced by anomalous scattering do not
follow the same symmetries as absorption and the other affects
corrected for by SADABS.)
Use a centrosymmetric point
group for error model and statistics [Y]: <CR> As with merging
Friedel opposites, you need a high data redundancy here, simply
applying
a centrosymmetric correction will generally work well in most cases.
Read reflection files written by SAINT (.raw assumed if no extension)
Enter filename (/ if no more) [ ]: filename0<CR>
Enter filename (/ if no more) [filename1.raw]: <CR>
Enter filename (/ if no more) [filename2.raw]: <CR>
Enter filename (/ if no more) [filename3.raw]: <CR>
Enter filename (/ if no more)
[filename4.raw]: /<CR>(Note
the "/" mark before the <CR>.)
This will read in the raw data from your integration and will allow you to begin the absorption correction process. You will then be presented with a table of information regarding your dataset. It will contain the number of data collected, the number of unique data, the number of redundant reflections (i.e. how many reflections were measured multiple times) and the number of reflections at a given intensity [I/sigma(I)].
It is worth noting down the
number of data collected and the number of unique reflections.
You will then be presented
with a series of questions regarding how to apply an absorption
correction to your data. Below is listed our recommended
defaults.
The sets of variables that most influence your data (and hence
are the most likely to change) are the mean(I/sigma) threshold (though
using a value of 5 results in
a
fairly accurate analysis by the software) and the odd and even
spherical harmonics. Generally a [6,1] harmonic yields the most
adequate correction. The two values should be altered
systematically and the resulting R(int) after the corrections are
applied should be noted. A gain of a few units in the last
decimal
place of R(int) is not a significant change and you should probably
return to an earlier harmonic correction.
Enter mean(I/sigma) threshold
(must be positive) [3]: 5<CR>
Highest resolution for parameter refinement [0.1]: <CR>
Factor g for initial weighting scheme w =
1/(sigma^2(I)+(g<I>)^2), where
sigma(I) is estimated by SAINT and <I> is mean intensity [0.04]: <CR>
The following restraint esd could be increased for strong absorbers.
Restraint esd for equal consecutive scale factors [0.005]: <CR>
Suitable spherical harmonic orders are 4,1 for weak absorption and 8,5
for
strong. Highest even order for spherical harmonics (0,2,4,6 or 8)
[6]: <CR>
Highest odd order for spherical harmonics (0,1,3,5 or 7) [3]: 1<CR>
Allow for crystal decomposition by B-value refinement [N]: <CR>
Number of refinement cycles [15]: <CR>
nnnn Reflections employed for parameter determination
Effective data to parameter ratio =x.yy
R(int) = 0.nnn before
parameter refinement
<List of R(int)'s across
each of the succesive cycles>
R(int) = 0.mmm
(selected reflections only, after parameter refinement).
(Another useful number to note down, the final R(int) of the data
set after the absorption correction has been applied.)
(At this point you can
either do as follows and write out the processed data, or you can test
other parameters by Repeating the analysis. If your crystal shape is
unusual or you just want to test the results, try increasing the number
of even coefficients.)
Repeat parameter
refinement (R) or accept (A) [A]: <CR>
[or R<CR> (to repeat
the
parameter refinement)]
You will now begin the
second portion of data analysis and correction;
PART 2 - Reject outliers and establish error model
High resolution limit
[0.1]:<CR> If your
data were weaker than you expected when you integrated the data (for
example if you integrated the data to 0.8 A and after analysis of the SAINT output it was revealed that the real
resolution was approximately 0.95 A) you could apply the high angle
cut-off here if you so choose.
|I-<I>|/su ratio for
rejection [4.0]: 10<CR>
This determines the upper limit for seriously erroneous data.
Setting this value to 10 allows more "outliers" to be included in
the dataset, or in another way to look at it, more of the original data
to be included in the final dataset.
g-value: (accept the default
at this stage).
You will then be given a new
g-value based on the software's own calculations. You should
accept the default.
A table detailing each block
of data, the R(int), calculated transmission factors, goodness of Fit
(of the data), the number of data in each block and the number of
strong
[I>2sigma(I)] data. For example:
Run 2-theta R(int) Incid. factors Diffr.
factors K Total I>2sig(I)
1 -25.0 0.0621 1.323 -
1.464 0.911 - 1.067 0.767
9968 5254
2 -25.0 0.0684 1.379 -
1.524 0.910 - 1.061 0.812
7126 3664
3 -25.0 0.0675 0.435 -
0.502 0.936 - 1.060 0.786
3718 1851
4 -25.0 0.0605 0.376 -
0.393 0.942 - 1.054
0.734 916 511
You can then be asked if you
wish to repeat the absorption correction process/parmeter refinement (P), repeat the rejection criteria
process (R) or to continue (A to accept).
When you choose to accept the
data model you have established, you will begin the final section of
the
program, writing out relevant data.
PART 3 - Output Postscript
diagnostics and corrected data
Write Postscript
diagnostic file (Y or N) [Y]: You choose. This function
creates a postscript image that can be printed out. It contains
information about the quality of the data across the entire data
collection. Generally not useful unless you suspect something
seriously wrong with your data (for example if the R(int)
of one of the blocks was significantly different from the rest)
Repeat (R), write .hkl file (W) or quit (Q) [W]: <CR>
Enter name of output .hkl file [sad.hkl]: filenames.hkl<CR> (NOTE: an "s" is used here to indicate that the data were processed using sadabs, you can use any name, but simply be careful not to over-write any other data).
Mu*r of equivalent
sphere for additional spherical absorption correction.
Enter <CR> if none: n.nn<CR>
(Enter the value that you calculate based on mu from XPREP and the
average radius of crystal)
Lambda/2 correction
factor (0 if none, e.g. for MWPC!) [0.0015]: <CR> This correction can
be modified if you collect data on a different diffractometer (0.0015
is
the correct value for the laboratory instruments). For example, data
collected at beamline 11.3.1
the
Advanced Light Source should have a lambda/2 correction factor of 0
(zero) applied.
xxxx Corrected reflections written to file filenames.hkl
Minimum/Maximum effective transmission: y.yyyyy
Repeat (R), write .hkl file (W) or quit (Q) [Q]: <CR> (This returns you to the system prompt.)
<...smartuse/mydir>%
Print the results of your analysis by typing
<...smartuse/mydir> %print filenames.out<CR>
Now back up your frames to CD, following the data archiving procedures.
Now move on to creating an account on BlueCHEX and solving your dataset.
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